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Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
其他题名Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
LI YAN1; LIU ZHIHAI1; LI JIE1; HAN LI1; LIU JIE1; ZHAO ZHIXIONG1; Wang RX(王任小)1
2014
发表期刊J. Chem Inf. Model.
卷号54期号:6页码:1700-1716
摘要Scoring functions are often applied in combination with molecular docking methods to predict ligand binding poses and ligand binding affinities or to identify active compounds through virtual screening. An objective benchmark for assessing the performance of current scoring functions is expected to provide practical guidance for the users to make smart choices among available methods. It can also elucidate the common weakness in current methods for future improvements. The primary goal of our comparative assessment of scoring functions (CASF) project is to provide a high-standard, publicly accessible benchmark of this type. Our latest study, i.e., CASF-2013, evaluated 20 popular scoring functions on an updated set of protein-ligand complexes. This data set was selected out of 8302 protein-ligand complexes recorded in the PDBbind database (version 2013) through a fairly complicated process. Sample selection was made by considering the quality of complex structures as well as binding data. Finally, qualified complexes were clustered by 90% similarity in protein sequences. Three representative complexes were chosen from each cluster to control sample redundancy. The final outcome, namely, the PDBbind core set (version 2013), consists of 195 protein ligand complexes in 65 clusters with binding constants spanning nearly 10 orders of magnitude. In this data set, 82% of the ligand molecules are "druglike" and 78% of the protein molecules are validated or potential drug targets. Correlation between binding constants and several key properties of ligands are discussed. Methods and results of the scoring function evaluation will be described in a companion work in this issue (doi: 10.1021/ci500081m).
学科领域计算机化学
DOI10.1021/ci500080q
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收录类别SCI
语种英语
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文献类型期刊论文
条目标识符http://ir.sioc.ac.cn/handle/331003/38924
专题计算机化学与化学信息学研究室
通讯作者Wang RX(王任小)
作者单位1.中科院上海有机化学研究所
2.澳门科技大学
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GB/T 7714
LI YAN,LIU ZHIHAI,LI JIE,et al. Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set[J]. J. Chem Inf. Model.,2014,54(6):1700-1716.
APA LI YAN.,LIU ZHIHAI.,LI JIE.,HAN LI.,LIU JIE.,...&王任小.(2014).Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set.J. Chem Inf. Model.,54(6),1700-1716.
MLA LI YAN,et al."Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set".J. Chem Inf. Model. 54.6(2014):1700-1716.
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